15-78849442-T-C

Variant names:

• chr15-78849442-T-C
• rs7173743
• ENST00000379535.8:c.115+8767T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000379535.8(MORF4L1):​c.115+8767T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.45 in 151,180 control chromosomes in the GnomAD database, including 15,562 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.45 (15562 hom., cov: 29)
• Consequence: MORF4L1 ENST00000379535.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.67
• Publications: 80 publications found

Genes affected

MORF4L1 (HGNC:16989): (mortality factor 4 like 1) Enables protein N-terminus binding activity. Involved in double-strand break repair via homologous recombination and histone modification. Located in nuclear speck. Part of NuA4 histone acetyltransferase complex and Sin3 complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MORF4L1	ENST00000379535.8	c.115+8767T>C		intron_variant	Intron 2 of 12	2		ENSP00000368850.4
MORF4L1	ENST00000559697.5	n.415+1361T>C		intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68024 AN: 151062 Hom.: 15547 Cov.: 29

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.475

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.450 AC: 68074 AN: 151180 Hom.: 15562 Cov.: 29 AF XY: 0.446 AC XY: 32913 AN XY: 73754

African (AFR) AF: 0.447 AC: 18394 AN: 41110

American (AMR) AF: 0.498 AC: 7540 AN: 15152

Ashkenazi Jewish (ASJ) AF: 0.505 AC: 1748 AN: 3464

East Asian (EAS) AF: 0.501 AC: 2567 AN: 5126

South Asian (SAS) AF: 0.372 AC: 1775 AN: 4776

European-Finnish (FIN) AF: 0.339 AC: 3508 AN: 10358

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.456 AC: 30934 AN: 67880

Other (OTH) AF: 0.470 AC: 992 AN: 2112

Alfa AF: 0.451 Hom.: 32567

Bravo AF: 0.464

Asia WGS AF: 0.419 AC: 1456 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.35
DANN	Benign	0.61
PhyloP100		-2.7
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7173743; hg19: chr15-79141784;